velocyto-team/velocyto.py

Issues

• Integrating Ambient RNA Removal (CellBender) into Velocity Analysis

  #403 opened 25 days ago by Evenlyeven
  0

• Merging multiple loom files with different reference genome

  #402 opened a month ago by yechanYS
  0

• Retriving genes with caracterisitic velocity behavior accorindg to latent time

  #401 opened a month ago by Dalhte
  0

• Incorrect trimming of chromosome name leads to IOError(f"Input .bam file should be chromosome-sorted. (Hint: use `samtools sort {bamfile}`)")

  #395 opened 3 months ago by kepbod
  3

• When calculate the unspliced reads, does UTR region included or not?

  #400 opened 2 months ago by DieTANG
  0

• Package dependency problem on NumPy

  #397 opened 2 months ago by jasonleongbio
  2

• Memory & run time issue run10x

  #399 opened 2 months ago by DelongZHOU
  1

• ImportError: speedboosted.cpython-38-x86_64-linux-gnu.so: undefined symbol: __log10_finite

  #377 opened 10 months ago by lili03080317
  2

• Velocyto ran successfully but main matrix is missing

  #398 opened 2 months ago by econnolly7
  2

• How to get fastq header information of spliced and unspliced 10X short reads

  #396 opened 3 months ago by wenhu0701
  0

• velocyto Index Out of Range

  #367 opened a year ago by TamaraSall
  2

• Mark spliced/unspliced reads on original BAM file

  #394 opened 3 months ago by taffy-miao
  0

• Seems like a typo.

  #393 opened 4 months ago by chenqiuhao
  0

• WARNING - The .bam file refers to a chromosome not present in the annotation (.gtf) file

  #388 opened 7 months ago by sekekeretsu
  4

• Additional gene problem

  #392 opened 4 months ago by Cadaqoes
  0

• Using spatial transcriptomics data on Velocyto.py generates lower counts than Space Ranger

  #391 opened 4 months ago by biyang-bioinfo
  0

• Inquiry on the input for running "velocyto run10x"

  #390 opened 4 months ago by daisyko
  0

• Error when running velocyto run-smartseq2

  #359 opened a year ago by ETAOIK
  1

• index file

  #386 opened 8 months ago by sherinesaber
  1

• velocyto on filtered or raw matrix or from matrix corrected ?

  #389 opened 5 months ago by Sirin24
  0

• High % of unspliced from 10X scRNAseq in tissues

  #364 opened a year ago by denvercal1234GitHub
  5

• Get tons of warnings when running

  #376 opened a year ago by dingyaozhang
  1

• Issues running velocyto

  #366 opened a year ago by Battamama
  1

• OSError: truncated file is occured in cellranger-5.0.1-dirty output.

  #387 opened 7 months ago by ilovegreentea
  0

• Unable to run velocyto: samtools issue

  #380 opened 10 months ago by millerkaplanlab
  1

• how do i generate the repeat sequences masked gtf file from Ensembl?

  #385 opened 8 months ago by erzakiev
  0

• When and when not to use "repeat annotation mask" in 10X?

  #384 opened 9 months ago by denvercal1234GitHub
  0

• Question about latent parameter t

  #383 opened 9 months ago by taffy-miao
  0

• BlockingIOError: [Errno 35] 'Resource temporarily unavailable' on Mac OS X

  #382 opened 9 months ago by YitengDang
  0

• [E::bgzf_read_block] Failed to read BGZF header at offset X

  #381 opened 9 months ago by YitengDang
  1

• possorted_genome_bam.bam file not found in cellranger output folder

  #360 opened a year ago by tangybat
  1

• how velocyto fits to cellrange-arc output

  #362 opened a year ago by zqmiao-mzq
  2

• TypeError: create() got an unexpected keyword argument 'matrix'

  #379 opened 10 months ago by zcaiwei
  0

• Passing velocyto samtools memory for sorting step

  #378 opened 10 months ago by wudustan
  0

• Batch effects in combining multiple loom files

  #375 opened a year ago by anshu957
  2

• ERRORS when running velocyto: ERROR - This is an older version of cellranger, cannot check if the output are ready, make sure of this yourself! ERROR - Can not locate the barcodes.tsv file!

  #358 opened a year ago by AsyaTiho
  2

• Running velocyto on 10x Cell Ranger cloud-generated files

  #371 opened a year ago by schroeme
  4

• ValueError: Column attribute 'Clusters' is not the same length (0) as number of columns in main matrix (3708)

  #374 opened a year ago by denvercal1234GitHub
  0

• Error in run10X: logging.debug(f"Example of barcode: {valid_bcs_list[0].split('-')[0]} and cell_id: {valid_cellid_list[0]}") - IndexError: list index out of range

  #373 opened a year ago by denvercal1234GitHub
  1

• AttributeError: 'NoneType' object has no attribute 'group'

  #372 opened a year ago by danli349
  0

• Fresh Installation is not working

  #352 opened 2 years ago by adRn-s
  1

• memory samtools problems in velocyto run

  #354 opened 2 years ago by ElenaSLuis
  1

• Failed to install velocyto on macOS

  #351 opened 2 years ago by r-osorio
  4

• Compatibility with non-string form for barcodes and UMIs

  #369 opened a year ago by weir12
  0

• Multi-omic

  #368 opened a year ago by zhangqc723
  0

• Unexpected MemoryError: bam file #0 could not be sorted by cells.

  #365 opened a year ago by monica-nicolau
  0

• meanings of layers

  #361 opened a year ago by songmingl
  2

• gene name issue

  #357 opened a year ago by YichaoOU
  1

• CellRanger --include-introns

  #356 opened 2 years ago by GEmilioHO
  0

• UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb2 in position 0: invalid start byte

  #353 opened 2 years ago by nroak
  0